1SI8

Crystal structure of E. faecalis catalase

• PDB DOI: https://doi.org/10.2210/pdb1SI8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Enterococcus faecalis V583
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2004-02-28 Released: 2004-05-04 
• Deposition Author(s): Hakansson, K.O., Brugna, M., Tasse, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.218 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 

Starting Model: experimental

Literature

The three-dimensional structure of catalase from Enterococcus faecalis.

Hakansson, K.O., Brugna, M., Tasse, L.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1374-1380

• PubMed: 15272159 
• DOI: https://doi.org/10.1107/S0907444904012004
• Primary Citation of Related Structures:  
  1SI8


• PubMed Abstract: 
  

  Enterococcus faecalis haem catalase was crystallized using lithium sulfate at neutral pH. The crystals belong to space group R3, with unit-cell parameters a = b = 236.9, c = 198.1 A. The three-dimensional structure was determined by molecular replacement using a subunit of the Proteus mirabilis catalase structure. It was refined against 2.3 A synchrotron data to a free R factor of 21.8%. Like other catalases, the E. faecalis catalase is a homotetramer with a fold and structure similar to those of its structurally closest relative P. mirabilis. The solvent structure in the active site is identical in the four subunits but differs from that found in other catalases. The structural consequences of the Ramachandran outlier Ser196 are discussed.

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Organizational Affiliation: 

August Krogh Institute, Copenhagen University, Universitetsparken 13, DK-2100 Kbh O, Denmark. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 222.02 kDa 
• Atom Count: 16,509 
• Modelled Residue Count: 1,896 
• Deposited Residue Count: 1,936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase	A, B, C, D	484	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: katA EC: 1.11.1.6
UniProt
Find proteins for Q834P5 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q834P5  Go to UniProtKB:  Q834P5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	H [auth A], K [auth B], O [auth C], R [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	E [auth A], F [auth A], I [auth B], J [auth B], L [auth C], M [auth C], P [auth D], Q [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	G [auth A], N [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.218 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 236.86	α = 90
b = 236.86	β = 90
c = 198.07	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-04 
Deposition Author(s): Hakansson, K.O., Brugna, M., Tasse, L.

Revision History  

• Version 1.0: 2004-05-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description